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The accuracy of TopHat is not affected by read length.
We detected gaps larger than those recovered by read mapping with BLAT.
Suspenders sorts the BAM files by read name and systematically compares each alternative mapping.
Exons too short to be identified by read alignment are identified by Tophat junction alignments.
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This approach consists of TR mapping with subsequent SNP-cleanup by read-backmapping to the WG.
Read-by-read analysis never identified this number of variants, so pseudogene contamination is extremely unlikely in our dataset.
They also capture flanking exons by read-through transcription.
All repeat regions were bridged by read-pairs or end-sequenced polymerase chain reaction (PCR) products.
All identified repeats were bridged by read-pairs or end-sequenced polymerase chain reaction (PCR) products.
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Since I tried Ludwig back in 2017, I have been constantly using it in both editing and translation. Ever since, I suggest it to my translators at ProSciEditing.

Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com